/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; import java.io.*; import java.net.*; import java.util.*; import java.util.jar.*; import javax.swing.*; import org.exolab.castor.xml.*; import uk.ac.vamsas.objects.utils.MapList; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; import jalview.schemes.*; import jalview.structure.StructureSelectionManager; /** * Write out the current jalview desktop state * as a Jalview XML stream. * * Note: the vamsas objects referred to here are primitive * versions of the VAMSAS project schema elements - they are * not the same and most likely never will be :) * * @author $author$ * @version $Revision$ */ public class Jalview2XML { /** * create/return unique hash string for sq * @param sq * @return new or existing unique string for sq */ String seqHash(SequenceI sq) { if (seqsToIds==null) { initSeqRefs(); } if (seqsToIds.containsKey(sq)) { return (String) seqsToIds.get(sq); } else { // create sequential key String key = "sq"+(seqsToIds.size()+1); seqsToIds.put(sq, key); return key; } } void clearSeqRefs() { seqRefIds.clear(); seqsToIds.clear(); } void initSeqRefs() { if (seqsToIds==null) { seqsToIds = new IdentityHashMap(); } if (seqRefIds==null) { seqRefIds = new Hashtable(); } } java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution java.util.Hashtable seqRefIds = null; // key->SequenceI resolution Vector frefedSequence = null; boolean raiseGUI = true; // whether errors are raised in dialog boxes or not public Jalview2XML() { } public Jalview2XML(boolean raiseGUI) { this.raiseGUI = raiseGUI; } public void resolveFrefedSequences() { if (frefedSequence.size() > 0) { int r = 0, rSize = frefedSequence.size(); while (r < rSize) { Object[] ref = (Object[]) frefedSequence.elementAt(r); if (ref != null) { String sref = (String) ref[0]; if (seqRefIds.containsKey(sref)) { if (ref[1] instanceof jalview.datamodel.Mapping) { SequenceI seq = (SequenceI) seqRefIds.get(sref); while (seq.getDatasetSequence() != null) { seq = seq.getDatasetSequence(); } ((jalview.datamodel.Mapping) ref[1]).setTo(seq); } else { System.err .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for " + ref[1].getClass() + " type objects."); } frefedSequence.remove(r); rSize--; } else { r++; } } else { frefedSequence.remove(r); rSize--; } } } } /** * This maintains a list of viewports, the key being the * seqSetId. Important to set historyItem and redoList * for multiple views */ Hashtable viewportsAdded; Hashtable annotationIds = new Hashtable(); String uniqueSetSuffix = ""; /** * List of pdbfiles added to Jar */ Vector pdbfiles = null; // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE public void SaveState(File statefile) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) { return; } try { FileOutputStream fos = new FileOutputStream(statefile); JarOutputStream jout = new JarOutputStream(fos); //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS //////////////////////////////////////////////////// //NOTE ALSO new PrintWriter must be used for each new JarEntry PrintWriter out = null; Vector shortNames = new Vector(); //REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { if (frames[i] instanceof AlignFrame) { AlignFrame af = (AlignFrame) frames[i]; String shortName = af.getTitle(); if (shortName.indexOf(File.separatorChar) > -1) { shortName = shortName.substring(shortName .lastIndexOf(File.separatorChar) + 1); } int count = 1; while (shortNames.contains(shortName)) { if (shortName.endsWith("_" + (count - 1))) { shortName = shortName .substring(0, shortName.lastIndexOf("_")); } shortName = shortName.concat("_" + count); count++; } shortNames.addElement(shortName); if (!shortName.endsWith(".xml")) { shortName = shortName + ".xml"; } int ap, apSize = af.alignPanels.size(); for (ap = 0; ap < apSize; ap++) { AlignmentPanel apanel = (AlignmentPanel) af.alignPanels .elementAt(ap); String fileName = apSize == 1 ? shortName : ap + shortName; if (!fileName.endsWith(".xml")) { fileName = fileName + ".xml"; } JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8")); SaveState(apanel, fileName, jout, out); } } } try { out.flush(); } catch (Exception foo) {}; jout.closeEntry(); try { jout.flush(); } catch (Exception foo) {}; jout.close(); } catch (Exception ex) { //TODO: inform user of the problem - they need to know if their data was not saved ! ex.printStackTrace(); } } // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW public boolean SaveAlignment(AlignFrame af, String jarFile, String fileName) { try { int ap, apSize = af.alignPanels.size(); FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); for (ap = 0; ap < apSize; ap++) { AlignmentPanel apanel = (AlignmentPanel) af.alignPanels .elementAt(ap); String jfileName = apSize == 1 ? fileName : fileName + ap; if (!jfileName.endsWith(".xml")) { jfileName = jfileName + ".xml"; } JarEntry entry = new JarEntry(jfileName); jout.putNextEntry(entry); PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8")); SaveState(apanel, jfileName, jout, out); try { out.flush(); } catch (Exception foo) {}; jout.closeEntry(); } try { jout.flush(); } catch (Exception foo) {}; jout.close(); return true; } catch (Exception ex) { ex.printStackTrace(); return false; } } /** * DOCUMENT ME! * * @param af DOCUMENT ME! * @param timeStamp DOCUMENT ME! * @param fileName DOCUMENT ME! * @param jout DOCUMENT ME! * @param out DOCUMENT ME! */ public JalviewModel SaveState(AlignmentPanel ap, String fileName, JarOutputStream jout, PrintWriter out) { initSeqRefs(); Vector userColours = new Vector(); AlignViewport av = ap.av; JalviewModel object = new JalviewModel(); object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); object.setCreationDate(new java.util.Date(System.currentTimeMillis())); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); jalview.datamodel.AlignmentI jal = av.alignment; if (av.hasHiddenRows) { jal = jal.getHiddenSequences().getFullAlignment(); } SequenceSet vamsasSet = new SequenceSet(); Sequence vamsasSeq; JalviewModelSequence jms = new JalviewModelSequence(); vamsasSet.setGapChar(jal.getGapCharacter() + ""); if (jal.getDataset() != null) { // dataset id is the dataset's hashcode vamsasSet.setDatasetId(jal.getDataset().hashCode() + ""); } if (jal.getProperties() != null) { Enumeration en = jal.getProperties().keys(); while (en.hasMoreElements()) { String key = en.nextElement().toString(); SequenceSetProperties ssp = new SequenceSetProperties(); ssp.setKey(key); ssp.setValue(jal.getProperties().get(key).toString()); vamsasSet.addSequenceSetProperties(ssp); } } JSeq jseq; //SAVE SEQUENCES String id = ""; jalview.datamodel.SequenceI jds; for (int i = 0; i < jal.getHeight(); i++) { jds = jal.getSequenceAt(i); id = seqHash(jds); if (seqRefIds.get(id) != null) { // This happens for two reasons: 1. multiple views are being serialised. 2. the hashCode has collided with another sequence's code. This DOES HAPPEN! (PF00072.15.stk does this) // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions. //System.err.println("vamsasSeq backref: "+id+""); //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString()); //System.err.println("Hashcode: "+seqHash(jds)); //SequenceI rsq = (SequenceI) seqRefIds.get(id + ""); //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString()); //System.err.println("Hashcode: "+seqHash(rsq)); } else { vamsasSeq = createVamsasSequence(id, jds); vamsasSet.addSequence(vamsasSeq); seqRefIds.put(id, jds); } jseq = new JSeq(); jseq.setStart(jds.getStart()); jseq.setEnd(jds.getEnd()); jseq.setColour(av.getSequenceColour(jds).getRGB()); jseq.setId(id); // jseq id should be a string not a number if (av.hasHiddenRows) { jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); if (av.hiddenRepSequences != null && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i))) { jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences .get(jal.getSequenceAt(i))).getSequencesInOrder(jal); for (int h = 0; h < reps.length; h++) { if (reps[h] != jal.getSequenceAt(i)) { jseq.addHiddenSequences(jal.findIndex(reps[h])); } } } } if (jds.getDatasetSequence().getSequenceFeatures() != null) { jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence() .getSequenceFeatures(); int index = 0; while (index < sf.length) { Features features = new Features(); features.setBegin(sf[index].getBegin()); features.setEnd(sf[index].getEnd()); features.setDescription(sf[index].getDescription()); features.setType(sf[index].getType()); features.setFeatureGroup(sf[index].getFeatureGroup()); features.setScore(sf[index].getScore()); if (sf[index].links != null) { for (int l = 0; l < sf[index].links.size(); l++) { OtherData keyValue = new OtherData(); keyValue.setKey("LINK_" + l); keyValue.setValue(sf[index].links.elementAt(l).toString()); features.addOtherData(keyValue); } } if (sf[index].otherDetails != null) { String key; Enumeration keys = sf[index].otherDetails.keys(); while (keys.hasMoreElements()) { key = keys.nextElement().toString(); OtherData keyValue = new OtherData(); keyValue.setKey(key); keyValue.setValue(sf[index].otherDetails.get(key).toString()); features.addOtherData(keyValue); } } jseq.addFeatures(features); index++; } } if (jds.getDatasetSequence().getPDBId() != null) { Enumeration en = jds.getDatasetSequence().getPDBId().elements(); while (en.hasMoreElements()) { Pdbids pdb = new Pdbids(); jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en .nextElement(); pdb.setId(entry.getId()); pdb.setType(entry.getType()); AppJmol jmol; //This must have been loaded, is it still visible? JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int f = frames.length - 1; f > -1; f--) { if (frames[f] instanceof AppJmol) { jmol = (AppJmol) frames[f]; if (!jmol.pdbentry.getId().equals(entry.getId())) continue; StructureState state = new StructureState(); state.setVisible(true); state.setXpos(jmol.getX()); state.setYpos(jmol.getY()); state.setWidth(jmol.getWidth()); state.setHeight(jmol.getHeight()); String statestring = jmol.viewer.getStateInfo(); if (state != null) { state.setContent(statestring.replaceAll("\n", "")); } for (int s = 0; s < jmol.sequence.length; s++) { if (jal.findIndex(jmol.sequence[s]) > -1) { pdb.addStructureState(state); } } } } if (entry.getFile() != null) { pdb.setFile(entry.getFile()); if (pdbfiles == null) { pdbfiles = new Vector(); } if (!pdbfiles.contains(entry.getId())) { pdbfiles.addElement(entry.getId()); try { File file = new File(entry.getFile()); if (file.exists() && jout != null) { byte[] data = new byte[(int) file.length()]; jout.putNextEntry(new JarEntry(entry.getId())); DataInputStream dis = new DataInputStream( new FileInputStream(file)); dis.readFully(data); DataOutputStream dout = new DataOutputStream(jout); dout.write(data, 0, data.length); dout.flush(); jout.closeEntry(); } } catch (Exception ex) { ex.printStackTrace(); } } } if (entry.getProperty() != null) { PdbentryItem item = new PdbentryItem(); Hashtable properties = entry.getProperty(); Enumeration en2 = properties.keys(); while (en2.hasMoreElements()) { Property prop = new Property(); String key = en2.nextElement().toString(); prop.setName(key); prop.setValue(properties.get(key).toString()); item.addProperty(prop); } pdb.addPdbentryItem(item); } jseq.addPdbids(pdb); } } jms.addJSeq(jseq); } if (av.hasHiddenRows) { jal = av.alignment; } // SAVE MAPPINGS if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0) { jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames(); for (int i = 0; i < jac.length; i++) { AlcodonFrame alc = new AlcodonFrame(); vamsasSet.addAlcodonFrame(alc); for (int p = 0; p < jac[i].aaWidth; p++) { Alcodon cmap = new Alcodon(); cmap.setPos1(jac[i].codons[p][0]); cmap.setPos2(jac[i].codons[p][1]); cmap.setPos3(jac[i].codons[p][2]); alc.addAlcodon(cmap); } if (jac[i].getProtMappings() != null && jac[i].getProtMappings().length > 0) { SequenceI[] dnas = jac[i].getdnaSeqs(); jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings(); for (int m = 0; m < pmaps.length; m++) { AlcodMap alcmap = new AlcodMap(); alcmap.setDnasq("" + dnas[m].hashCode()); alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, false)); alc.addAlcodMap(alcmap); } } } } //SAVE TREES /////////////////////////////////// if (av.currentTree != null) { // FIND ANY ASSOCIATED TREES // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT if (Desktop.desktop != null) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int t = 0; t < frames.length; t++) { if (frames[t] instanceof TreePanel) { TreePanel tp = (TreePanel) frames[t]; if (tp.treeCanvas.av.alignment == jal) { Tree tree = new Tree(); tree.setTitle(tp.getTitle()); tree.setCurrentTree((av.currentTree == tp.getTree())); tree.setNewick(tp.getTree().toString()); tree.setThreshold(tp.treeCanvas.threshold); tree.setFitToWindow(tp.fitToWindow.getState()); tree.setFontName(tp.getTreeFont().getName()); tree.setFontSize(tp.getTreeFont().getSize()); tree.setFontStyle(tp.getTreeFont().getStyle()); tree.setMarkUnlinked(tp.placeholdersMenu.getState()); tree.setShowBootstrap(tp.bootstrapMenu.getState()); tree.setShowDistances(tp.distanceMenu.getState()); tree.setHeight(tp.getHeight()); tree.setWidth(tp.getWidth()); tree.setXpos(tp.getX()); tree.setYpos(tp.getY()); jms.addTree(tree); } } } } } //SAVE ANNOTATIONS if (jal.getAlignmentAnnotation() != null) { jalview.datamodel.AlignmentAnnotation[] aa = jal .getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { Annotation an = new Annotation(); if (aa[i].annotationId != null) { annotationIds.put(aa[i].annotationId, aa[i]); } an.setId(aa[i].annotationId); if (aa[i] == av.quality || aa[i] == av.conservation || aa[i] == av.consensus) { an.setLabel(aa[i].label); an.setGraph(true); vamsasSet.addAnnotation(an); continue; } an.setVisible(aa[i].visible); an.setDescription(aa[i].description); if (aa[i].sequenceRef != null) { an.setSequenceRef(aa[i].sequenceRef.getName()); } if (aa[i].graph > 0) { an.setGraph(true); an.setGraphType(aa[i].graph); an.setGraphGroup(aa[i].graphGroup); if (aa[i].getThreshold() != null) { ThresholdLine line = new ThresholdLine(); line.setLabel(aa[i].getThreshold().label); line.setValue(aa[i].getThreshold().value); line.setColour(aa[i].getThreshold().colour.getRGB()); an.setThresholdLine(line); } } else { an.setGraph(false); } an.setLabel(aa[i].label); if (aa[i].hasScore()) { an.setScore(aa[i].getScore()); } AnnotationElement ae; if (aa[i].annotations != null) { an.setScoreOnly(false); for (int a = 0; a < aa[i].annotations.length; a++) { if ((aa[i] == null) || (aa[i].annotations[a] == null)) { continue; } ae = new AnnotationElement(); if (aa[i].annotations[a].description != null) ae.setDescription(aa[i].annotations[a].description); if (aa[i].annotations[a].displayCharacter != null) ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); if (!Float.isNaN(aa[i].annotations[a].value)) ae.setValue(aa[i].annotations[a].value); ae.setPosition(a); if (aa[i].annotations[a].secondaryStructure != ' ' && aa[i].annotations[a].secondaryStructure != '\0') ae .setSecondaryStructure(aa[i].annotations[a].secondaryStructure + ""); if (aa[i].annotations[a].colour != null && aa[i].annotations[a].colour != java.awt.Color.black) { ae.setColour(aa[i].annotations[a].colour.getRGB()); } an.addAnnotationElement(ae); } } else { an.setScoreOnly(true); } vamsasSet.addAnnotation(an); } } //SAVE GROUPS if (jal.getGroups() != null) { JGroup[] groups = new JGroup[jal.getGroups().size()]; for (int i = 0; i < groups.length; i++) { groups[i] = new JGroup(); jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal .getGroups().elementAt(i); groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); groups[i].setName(sg.getName()); if (sg.cs != null) { if (sg.cs.conservationApplied()) { groups[i].setConsThreshold(sg.cs.getConservationInc()); if (sg.cs instanceof jalview.schemes.UserColourScheme) { groups[i].setColour(SetUserColourScheme(sg.cs, userColours, jms)); } else { groups[i] .setColour(ColourSchemeProperty.getColourName(sg.cs)); } } else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) { groups[i] .setColour(ColourSchemeProperty .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs) .getBaseColour())); } else if (sg.cs instanceof jalview.schemes.UserColourScheme) { groups[i] .setColour(SetUserColourScheme(sg.cs, userColours, jms)); } else { groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs)); } groups[i].setPidThreshold(sg.cs.getThreshold()); } groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); groups[i].setDisplayBoxes(sg.getDisplayBoxes()); groups[i].setDisplayText(sg.getDisplayText()); groups[i].setColourText(sg.getColourText()); groups[i].setTextCol1(sg.textColour.getRGB()); groups[i].setTextCol2(sg.textColour2.getRGB()); groups[i].setTextColThreshold(sg.thresholdTextColour); for (int s = 0; s < sg.getSize(); s++) { jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg .getSequenceAt(s); groups[i].addSeq(seqHash(seq)); } } jms.setJGroup(groups); } ///////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(ap.alignFrame.getTitle()); view.setSequenceSetId(av.getSequenceSetId()); view.setViewName(av.viewName); view.setGatheredViews(av.gatherViewsHere); if (ap.av.explodedPosition != null) { view.setXpos(av.explodedPosition.x); view.setYpos(av.explodedPosition.y); view.setWidth(av.explodedPosition.width); view.setHeight(av.explodedPosition.height); } else { view.setXpos(ap.alignFrame.getBounds().x); view.setYpos(ap.alignFrame.getBounds().y); view.setWidth(ap.alignFrame.getBounds().width); view.setHeight(ap.alignFrame.getBounds().height); } view.setStartRes(av.startRes); view.setStartSeq(av.startSeq); if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), userColours, jms)); } else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) { jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av .getGlobalColourScheme(); AnnotationColours ac = new AnnotationColours(); ac.setAboveThreshold(acg.getAboveThreshold()); ac.setThreshold(acg.getAnnotationThreshold()); ac.setAnnotation(acg.getAnnotation()); if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme) { ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(), userColours, jms)); } else { ac.setColourScheme(ColourSchemeProperty.getColourName(acg .getBaseColour())); } ac.setMaxColour(acg.getMaxColour().getRGB()); ac.setMinColour(acg.getMinColour().getRGB()); view.setAnnotationColours(ac); view.setBgColour("AnnotationColourGradient"); } else { view.setBgColour(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); } ColourSchemeI cs = av.getGlobalColourScheme(); if (cs != null) { if (cs.conservationApplied()) { view.setConsThreshold(cs.getConservationInc()); if (cs instanceof jalview.schemes.UserColourScheme) { view.setBgColour(SetUserColourScheme(cs, userColours, jms)); } } if (cs instanceof ResidueColourScheme) { view.setPidThreshold(cs.getThreshold()); } } view.setConservationSelected(av.getConservationSelected()); view.setPidSelected(av.getAbovePIDThreshold()); view.setFontName(av.font.getName()); view.setFontSize(av.font.getSize()); view.setFontStyle(av.font.getStyle()); view.setRenderGaps(av.renderGaps); view.setShowAnnotation(av.getShowAnnotation()); view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowFullId(av.getShowJVSuffix()); view.setRightAlignIds(av.rightAlignIds); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); view.setWrapAlignment(av.getWrapAlignment()); view.setTextCol1(av.textColour.getRGB()); view.setTextCol2(av.textColour2.getRGB()); view.setTextColThreshold(av.thresholdTextColour); if (av.featuresDisplayed != null) { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; Vector settingsAdded = new Vector(); for (int ro = 0; ro < renderOrder.length; ro++) { Setting setting = new Setting(); setting.setType(renderOrder[ro]); setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() .getColour(renderOrder[ro]).getRGB()); setting.setDisplay(av.featuresDisplayed .containsKey(renderOrder[ro])); float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder( renderOrder[ro]); if (rorder > -1) { setting.setOrder(rorder); } fs.addSetting(setting); settingsAdded.addElement(renderOrder[ro]); } //Make sure we save none displayed feature settings Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours .keys(); while (en.hasMoreElements()) { String key = en.nextElement().toString(); if (settingsAdded.contains(key)) { continue; } Setting setting = new Setting(); setting.setType(key); setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() .getColour(key).getRGB()); setting.setDisplay(false); float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder( key); if (rorder > -1) { setting.setOrder(rorder); } fs.addSetting(setting); settingsAdded.addElement(key); } en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys(); Vector groupsAdded = new Vector(); while (en.hasMoreElements()) { String grp = en.nextElement().toString(); if (groupsAdded.contains(grp)) { continue; } Group g = new Group(); g.setName(grp); g .setDisplay(((Boolean) ap.seqPanel.seqCanvas .getFeatureRenderer().featureGroups.get(grp)) .booleanValue()); fs.addGroup(g); groupsAdded.addElement(grp); } jms.setFeatureSettings(fs); } if (av.hasHiddenColumns) { for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++) { int[] region = (int[]) av.getColumnSelection().getHiddenColumns() .elementAt(c); HiddenColumns hc = new HiddenColumns(); hc.setStart(region[0]); hc.setEnd(region[1]); view.addHiddenColumns(hc); } } jms.addViewport(view); object.setJalviewModelSequence(jms); object.getVamsasModel().addSequenceSet(vamsasSet); if (out != null) { //We may not want to write the object to disk, //eg we can copy the alignViewport to a new view object //using save and then load try { org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(out); marshaller.marshal(object); out.flush(); } catch (Exception ex) { ex.printStackTrace(); } } return object; } private Sequence createVamsasSequence(String id, SequenceI jds) { return createVamsasSequence(true, id, jds, null); } private Sequence createVamsasSequence(boolean recurse, String id, SequenceI jds, SequenceI parentseq) { Sequence vamsasSeq = new Sequence(); vamsasSeq.setId(id); vamsasSeq.setName(jds.getName()); vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); jalview.datamodel.DBRefEntry[] dbrefs = null; if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); if (jds.getDatasetSequence().getDBRef() != null) { dbrefs = jds.getDatasetSequence().getDBRef(); } } else { vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only dbrefs = jds.getDBRef(); } if (dbrefs != null) { for (int d = 0; d < dbrefs.length; d++) { DBRef dbref = new DBRef(); dbref.setSource(dbrefs[d].getSource()); dbref.setVersion(dbrefs[d].getVersion()); dbref.setAccessionId(dbrefs[d].getAccessionId()); if (dbrefs[d].hasMap()) { Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, jds, recurse); dbref.setMapping(mp); } vamsasSeq.addDBRef(dbref); } } return vamsasSeq; } private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp, SequenceI parentseq, SequenceI jds, boolean recurse) { Mapping mp = null; if (jmp.getMap() != null) { mp = new Mapping(); jalview.util.MapList mlst = jmp.getMap(); int r[] = mlst.getFromRanges(); for (int s = 0; s < r.length; s += 2) { MapListFrom mfrom = new MapListFrom(); mfrom.setStart(r[s]); mfrom.setEnd(r[s + 1]); mp.addMapListFrom(mfrom); } r = mlst.getToRanges(); for (int s = 0; s < r.length; s += 2) { MapListTo mto = new MapListTo(); mto.setStart(r[s]); mto.setEnd(r[s + 1]); mp.addMapListTo(mto); } mp.setMapFromUnit(mlst.getFromRatio()); mp.setMapToUnit(mlst.getToRatio()); if (jmp.getTo() != null) { MappingChoice mpc = new MappingChoice(); if (recurse && (parentseq != jmp.getTo() || parentseq .getDatasetSequence() != jmp.getTo())) { mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()) , jmp.getTo(), jds)); } else { String jmpid = ""; SequenceI ps = null; if (parentseq != jmp.getTo() && parentseq.getDatasetSequence() != jmp.getTo()) { // chaining dbref rather than a handshaking one jmpid = seqHash(ps = jmp.getTo()); } else { jmpid = seqHash(ps = parentseq); } mpc.setDseqFor(jmpid); if (!seqRefIds.containsKey(mpc.getDseqFor())) { jalview.bin.Cache.log.debug("creatign new DseqFor ID"); seqRefIds.put(mpc.getDseqFor(), ps); } else { jalview.bin.Cache.log.debug("reusing DseqFor ID"); } } mp.setMappingChoice(mpc); } } return mp; } String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, Vector userColours, JalviewModelSequence jms) { String id = null; jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; if (!userColours.contains(ucs)) { userColours.add(ucs); java.awt.Color[] colours = ucs.getColours(); jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); for (int i = 0; i < colours.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(ResidueProperties.aa[i]); col.setRGB(jalview.util.Format.getHexString(colours[i])); jbucs.addColour(col); } if (ucs.getLowerCaseColours() != null) { colours = ucs.getLowerCaseColours(); for (int i = 0; i < colours.length; i++) { jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setName(ResidueProperties.aa[i].toLowerCase()); col.setRGB(jalview.util.Format.getHexString(colours[i])); jbucs.addColour(col); } } id = "ucs" + userColours.indexOf(ucs); uc.setId(id); uc.setUserColourScheme(jbucs); jms.addUserColours(uc); } return id; } jalview.schemes.UserColourScheme GetUserColourScheme( JalviewModelSequence jms, String id) { UserColours[] uc = jms.getUserColours(); UserColours colours = null; for (int i = 0; i < uc.length; i++) { if (uc[i].getId().equals(id)) { colours = uc[i]; break; } } java.awt.Color[] newColours = new java.awt.Color[24]; for (int i = 0; i < 24; i++) { newColours[i] = new java.awt.Color(Integer.parseInt(colours .getUserColourScheme().getColour(i).getRGB(), 16)); } jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( newColours); if (colours.getUserColourScheme().getColourCount() > 24) { newColours = new java.awt.Color[23]; for (int i = 0; i < 23; i++) { newColours[i] = new java.awt.Color(Integer.parseInt(colours .getUserColourScheme().getColour(i + 24).getRGB(), 16)); } ucs.setLowerCaseColours(newColours); } return ucs; } /** * DOCUMENT ME! * * @param file DOCUMENT ME! */ public AlignFrame LoadJalviewAlign(final String file) { uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; jalview.gui.AlignFrame af = null; seqRefIds = new Hashtable(); viewportsAdded = new Hashtable(); frefedSequence = new Vector(); Hashtable gatherToThisFrame = new Hashtable(); String errorMessage = null; try { //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING URL url = null; if (file.startsWith("http://")) { url = new URL(file); } JarInputStream jin = null; JarEntry jarentry = null; int entryCount = 1; do { if (url != null) { jin = new JarInputStream(url.openStream()); } else { jin = new JarInputStream(new FileInputStream(file)); } for (int i = 0; i < entryCount; i++) { jarentry = jin.getNextJarEntry(); } if (jarentry != null && jarentry.getName().endsWith(".xml")) { InputStreamReader in = new InputStreamReader(jin, "UTF-8"); JalviewModel object = new JalviewModel(); Unmarshaller unmar = new Unmarshaller(object); unmar.setValidation(false); object = (JalviewModel) unmar.unmarshal(in); af = LoadFromObject(object, file, true); if (af.viewport.gatherViewsHere) { gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); } entryCount++; } else if (jarentry != null) { //Some other file here. entryCount++; } } while (jarentry != null); resolveFrefedSequences(); } catch (java.io.FileNotFoundException ex) { ex.printStackTrace(); errorMessage = "Couldn't locate Jalview XML file : " + file; System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); } catch (java.net.UnknownHostException ex) { ex.printStackTrace(); errorMessage = "Couldn't locate Jalview XML file : " + file; System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); } catch (Exception ex) { //Is Version 1 Jar file? try { af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file); } catch (Exception ex2) { System.err.println("Exception whilst loading as jalviewXMLV1:"); ex2.printStackTrace(); af = null; } if (Desktop.instance != null) { Desktop.instance.stopLoading(); } if (af != null) { System.out.println("Successfully loaded archive file"); return af; } ex.printStackTrace(); System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); } if (Desktop.instance != null) { Desktop.instance.stopLoading(); } Enumeration en = gatherToThisFrame.elements(); while (en.hasMoreElements()) { Desktop.instance.gatherViews((AlignFrame) en.nextElement()); } if (errorMessage != null) { final String finalErrorMessage = errorMessage; if (raiseGUI) { javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, finalErrorMessage, "Error loading Jalview file", JOptionPane.WARNING_MESSAGE); } }); } else { System.err.println("Problem loading Jalview file: "+errorMessage); } } return af; } Hashtable alreadyLoadedPDB; String loadPDBFile(String file, String pdbId) { if (alreadyLoadedPDB == null) alreadyLoadedPDB = new Hashtable(); if (alreadyLoadedPDB.containsKey(pdbId)) return alreadyLoadedPDB.get(pdbId).toString(); try { JarInputStream jin = null; if (file.startsWith("http://")) { jin = new JarInputStream(new URL(file).openStream()); } else { jin = new JarInputStream(new FileInputStream(file)); } JarEntry entry = null; do { entry = jin.getNextJarEntry(); } while (!entry.getName().equals(pdbId)); BufferedReader in = new BufferedReader(new InputStreamReader(jin)); File outFile = File.createTempFile("jalview_pdb", ".txt"); outFile.deleteOnExit(); PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); String data; while ((data = in.readLine()) != null) { out.println(data); } try { out.flush(); } catch (Exception foo) {}; out.close(); alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); return outFile.getAbsolutePath(); } catch (Exception ex) { ex.printStackTrace(); } return null; } AlignFrame LoadFromObject(JalviewModel object, String file, boolean loadTreesAndStructures) { SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); Sequence[] vamsasSeq = vamsasSet.getSequence(); JalviewModelSequence jms = object.getJalviewModelSequence(); Viewport view = jms.getViewport(0); ////////////////////////////////// //LOAD SEQUENCES Vector hiddenSeqs = null; jalview.datamodel.Sequence jseq; ArrayList tmpseqs = new ArrayList(); boolean multipleView = false; JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); int vi=0; // counter in vamsasSeq array for (int i = 0; i < JSEQ.length; i++) { String seqId = JSEQ[i].getId() + ""; if (seqRefIds.get(seqId) != null) { tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId)); multipleView = true; } else { jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), vamsasSeq[vi].getSequence()); jseq.setDescription(vamsasSeq[vi].getDescription()); jseq.setStart(JSEQ[i].getStart()); jseq.setEnd(JSEQ[i].getEnd()); jseq.setVamsasId(uniqueSetSuffix + seqId); seqRefIds.put(vamsasSeq[vi].getId()+"", jseq); tmpseqs.add(jseq); vi++; } if (JSEQ[i].getHidden()) { if (hiddenSeqs == null) { hiddenSeqs = new Vector(); } hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds .get(seqId)); } } /// // Create the alignment object from the sequence set ///////////////////////////////// jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs .size()]; tmpseqs.toArray(orderedSeqs); jalview.datamodel.Alignment al = new jalview.datamodel.Alignment( orderedSeqs); /// Add the alignment properties for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) { SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i); al.setProperty(ssp.getKey(), ssp.getValue()); } /// // SequenceFeatures are added to the DatasetSequence, // so we must create or recover the dataset before loading features ///////////////////////////////// if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") { // older jalview projects do not have a dataset id. al.setDataset(null); } else { recoverDatasetFor(vamsasSet, al); } ///////////////////////////////// Hashtable pdbloaded = new Hashtable(); if (!multipleView) { for (int i = 0; i < vamsasSeq.length; i++) { if (JSEQ[i].getFeaturesCount() > 0) { Features[] features = JSEQ[i].getFeatures(); for (int f = 0; f < features.length; f++) { jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature( features[f].getType(), features[f].getDescription(), features[f].getStatus(), features[f].getBegin(), features[f].getEnd(), features[f].getFeatureGroup()); sf.setScore(features[f].getScore()); for (int od = 0; od < features[f].getOtherDataCount(); od++) { OtherData keyValue = features[f].getOtherData(od); if (keyValue.getKey().startsWith("LINK")) { sf.addLink(keyValue.getValue()); } else { sf.setValue(keyValue.getKey(), keyValue.getValue()); } } al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); } } if (vamsasSeq[i].getDBRefCount() > 0) { addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); } if (JSEQ[i].getPdbidsCount() > 0) { Pdbids[] ids = JSEQ[i].getPdbids(); for (int p = 0; p < ids.length; p++) { jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); entry.setId(ids[p].getId()); entry.setType(ids[p].getType()); if (ids[p].getFile() != null) { if (!pdbloaded.containsKey(ids[p].getFile())) { entry.setFile(loadPDBFile(file, ids[p].getId())); } else { entry.setFile(pdbloaded.get(ids[p].getId()).toString()); } } al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); } } } } ///////////////////////////////// // LOAD SEQUENCE MAPPINGS if (vamsasSet.getAlcodonFrameCount() > 0) { AlcodonFrame[] alc = vamsasSet.getAlcodonFrame(); for (int i = 0; i < alc.length; i++) { jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame( alc[i].getAlcodonCount()); if (alc[i].getAlcodonCount() > 0) { Alcodon[] alcods = alc[i].getAlcodon(); for (int p = 0; p < cf.codons.length; p++) { cf.codons[p] = new int[3]; cf.codons[p][0] = (int) alcods[p].getPos1(); cf.codons[p][1] = (int) alcods[p].getPos2(); cf.codons[p][2] = (int) alcods[p].getPos3(); } } if (alc[i].getAlcodMapCount() > 0) { AlcodMap[] maps = alc[i].getAlcodMap(); for (int m = 0; m < maps.length; m++) { SequenceI dnaseq = (SequenceI) seqRefIds .get(maps[m].getDnasq()); // Load Mapping // attach to dna sequence reference. if (dnaseq != null) { if (maps[m].getMapping() != null) { jalview.datamodel.Mapping mapping = addMapping(maps[m] .getMapping()); cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); } } } } al.addCodonFrame(cf); } } ////////////////////////////////// //LOAD ANNOTATIONS boolean hideQuality = true, hideConservation = true, hideConsensus = true; if (vamsasSet.getAnnotationCount() > 0) { Annotation[] an = vamsasSet.getAnnotation(); for (int i = 0; i < an.length; i++) { if (an[i].getLabel().equals("Quality")) { hideQuality = false; continue; } else if (an[i].getLabel().equals("Conservation")) { hideConservation = false; continue; } else if (an[i].getLabel().equals("Consensus")) { hideConsensus = false; continue; } if (an[i].getId() != null && annotationIds.containsKey(an[i].getId())) { jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds .get(an[i].getId()); if (an[i].hasVisible()) jda.visible = an[i].getVisible(); al.addAnnotation(jda); continue; } AnnotationElement[] ae = an[i].getAnnotationElement(); jalview.datamodel.Annotation[] anot = null; if (!an[i].getScoreOnly()) { anot = new jalview.datamodel.Annotation[al.getWidth()]; for (int aa = 0; aa < ae.length && aa < anot.length; aa++) { if (ae[aa].getPosition() >= anot.length) continue; anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa] .getSecondaryStructure() == null || ae[aa] .getSecondaryStructure().length() == 0) ? ' ' : ae[aa] .getSecondaryStructure().charAt(0), ae[aa].getValue() ); // JBPNote: Consider verifying dataflow for IO of secondary structure annotation read from Stockholm files // this was added to try to ensure that //if (anot[ae[aa].getPosition()].secondaryStructure>' ') //{ // anot[ae[aa].getPosition()].displayCharacter = ""; //} anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa] .getColour()); } } jalview.datamodel.AlignmentAnnotation jaa = null; if (an[i].getGraph()) { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot, 0, 0, an[i].getGraphType()); jaa.graphGroup = an[i].getGraphGroup(); if (an[i].getThresholdLine() != null) { jaa.setThreshold(new jalview.datamodel.GraphLine(an[i] .getThresholdLine().getValue(), an[i] .getThresholdLine().getLabel(), new java.awt.Color( an[i].getThresholdLine().getColour()))); } } else { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); } if (an[i].getId() != null) { annotationIds.put(an[i].getId(), jaa); jaa.annotationId = an[i].getId(); } if (an[i].getSequenceRef() != null) { if (al.findName(an[i].getSequenceRef()) != null) { jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()), 1, true); al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); } } if (an[i].hasScore()) { jaa.setScore(an[i].getScore()); } if (an[i].hasVisible()) jaa.visible = an[i].getVisible(); al.addAnnotation(jaa); } } ///////////////////////// //LOAD GROUPS if (jms.getJGroupCount() > 0) { JGroup[] groups = jms.getJGroup(); for (int i = 0; i < groups.length; i++) { ColourSchemeI cs = null; if (groups[i].getColour() != null) { if (groups[i].getColour().startsWith("ucs")) { cs = GetUserColourScheme(jms, groups[i].getColour()); } else { cs = ColourSchemeProperty.getColour(al, groups[i].getColour()); } if (cs != null) { cs.setThreshold(groups[i].getPidThreshold(), true); } } Vector seqs = new Vector(); for (int s = 0; s < groups[i].getSeqCount(); s++) { String seqId = groups[i].getSeq(s) + ""; jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds .get(seqId); if (ts != null) { seqs.addElement(ts); } } if (seqs.size() < 1) { continue; } jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup( seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(), groups[i].getDisplayText(), groups[i].getColourText(), groups[i].getStart(), groups[i].getEnd()); sg .setOutlineColour(new java.awt.Color(groups[i] .getOutlineColour())); sg.textColour = new java.awt.Color(groups[i].getTextCol1()); sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); sg.thresholdTextColour = groups[i].getTextColThreshold(); if (groups[i].getConsThreshold() != 0) { jalview.analysis.Conservation c = new jalview.analysis.Conservation( "All", ResidueProperties.propHash, 3, sg .getSequences(null), 0, sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); sg.cs.setConservation(c); } al.addGroup(sg); } } ///////////////////////////////// // LOAD VIEWPORT AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight()); af.setFileName(file, "Jalview"); for (int i = 0; i < JSEQ.length; i++) { af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); } //If we just load in the same jar file again, the sequenceSetId //will be the same, and we end up with multiple references //to the same sequenceSet. We must modify this id on load //so that each load of the file gives a unique id String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; af.viewport.gatherViewsHere = view.getGatheredViews(); if (view.getSequenceSetId() != null) { jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded .get(uniqueSeqSetId); af.viewport.sequenceSetID = uniqueSeqSetId; if (av != null) { af.viewport.historyList = av.historyList; af.viewport.redoList = av.redoList; } else { viewportsAdded.put(uniqueSeqSetId, af.viewport); } PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); } if (hiddenSeqs != null) { for (int s = 0; s < JSEQ.length; s++) { jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup(); for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) { hidden.addSequence(al .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false); } af.viewport.hideRepSequences(al.getSequenceAt(s), hidden); } jalview.datamodel.SequenceI[] hseqs = new jalview.datamodel.SequenceI[hiddenSeqs .size()]; for (int s = 0; s < hiddenSeqs.size(); s++) { hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s); } af.viewport.hideSequence(hseqs); } if ((hideConsensus || hideQuality || hideConservation) && al.getAlignmentAnnotation() != null) { int hSize = al.getAlignmentAnnotation().length; for (int h = 0; h < hSize; h++) { if ((hideConsensus && al.getAlignmentAnnotation()[h].label .equals("Consensus")) || (hideQuality && al.getAlignmentAnnotation()[h].label .equals("Quality")) || (hideConservation && al.getAlignmentAnnotation()[h].label .equals("Conservation"))) { al.deleteAnnotation(al.getAlignmentAnnotation()[h]); hSize--; h--; } } af.alignPanel.adjustAnnotationHeight(); } if (view.getViewName() != null) { af.viewport.viewName = view.getViewName(); af.setInitialTabVisible(); } af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view .getHeight()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.setAbovePIDThreshold(view.getPidSelected()); af.viewport.setColourText(view.getShowColourText()); af.viewport.setConservationSelected(view.getConservationSelected()); af.viewport.setShowJVSuffix(view.getShowFullId()); af.viewport.rightAlignIds = view.getRightAlignIds(); af.viewport.setFont(new java.awt.Font(view.getFontName(), view .getFontStyle(), view.getFontSize())); af.alignPanel.fontChanged(); af.viewport.setRenderGaps(view.getRenderGaps()); af.viewport.setWrapAlignment(view.getWrapAlignment()); af.alignPanel.setWrapAlignment(view.getWrapAlignment()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); af.viewport.setShowBoxes(view.getShowBoxes()); af.viewport.setShowText(view.getShowText()); af.viewport.textColour = new java.awt.Color(view.getTextCol1()); af.viewport.textColour2 = new java.awt.Color(view.getTextCol2()); af.viewport.thresholdTextColour = view.getTextColThreshold(); af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); ColourSchemeI cs = null; if (view.getBgColour() != null) { if (view.getBgColour().startsWith("ucs")) { cs = GetUserColourScheme(jms, view.getBgColour()); } else if (view.getBgColour().startsWith("Annotation")) { //int find annotation for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++) { if (af.viewport.alignment.getAlignmentAnnotation()[i].label .equals(view.getAnnotationColours().getAnnotation())) { if (af.viewport.alignment.getAlignmentAnnotation()[i] .getThreshold() == null) { af.viewport.alignment.getAlignmentAnnotation()[i] .setThreshold(new jalview.datamodel.GraphLine(view .getAnnotationColours().getThreshold(), "Threshold", java.awt.Color.black) ); } if (view.getAnnotationColours().getColourScheme() .equals("None")) { cs = new AnnotationColourGradient(af.viewport.alignment .getAlignmentAnnotation()[i], new java.awt.Color(view .getAnnotationColours().getMinColour()), new java.awt.Color(view.getAnnotationColours() .getMaxColour()), view.getAnnotationColours() .getAboveThreshold()); } else if (view.getAnnotationColours().getColourScheme() .startsWith("ucs")) { cs = new AnnotationColourGradient(af.viewport.alignment .getAlignmentAnnotation()[i], GetUserColourScheme( jms, view.getAnnotationColours().getColourScheme()), view.getAnnotationColours().getAboveThreshold()); } else { cs = new AnnotationColourGradient(af.viewport.alignment .getAlignmentAnnotation()[i], ColourSchemeProperty .getColour(al, view.getAnnotationColours() .getColourScheme()), view .getAnnotationColours().getAboveThreshold()); } // Also use these settings for all the groups if (al.getGroups() != null) { for (int g = 0; g < al.getGroups().size(); g++) { jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al .getGroups().elementAt(g); if (sg.cs == null) { continue; } /* if (view.getAnnotationColours().getColourScheme().equals("None")) { sg.cs = new AnnotationColourGradient( af.viewport.alignment.getAlignmentAnnotation()[i], new java.awt.Color(view.getAnnotationColours(). getMinColour()), new java.awt.Color(view.getAnnotationColours(). getMaxColour()), view.getAnnotationColours().getAboveThreshold()); } else*/ { sg.cs = new AnnotationColourGradient( af.viewport.alignment.getAlignmentAnnotation()[i], sg.cs, view.getAnnotationColours() .getAboveThreshold()); } } } break; } } } else { cs = ColourSchemeProperty.getColour(al, view.getBgColour()); } if (cs != null) { cs.setThreshold(view.getPidThreshold(), true); cs.setConsensus(af.viewport.hconsensus); } } af.viewport.setGlobalColourScheme(cs); af.viewport.setColourAppliesToAllGroups(false); if (view.getConservationSelected() && cs != null) { cs.setConservationInc(view.getConsThreshold()); } af.changeColour(cs); af.viewport.setColourAppliesToAllGroups(true); if (view.getShowSequenceFeatures()) { af.viewport.showSequenceFeatures = true; } if (jms.getFeatureSettings() != null) { af.viewport.featuresDisplayed = new Hashtable(); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( setting.getType(), new java.awt.Color(setting.getColour())); renderOrder[fs] = setting.getType(); if (setting.hasOrder()) af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( setting.getType(), setting.getOrder()); else af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( setting.getType(), fs / jms.getFeatureSettings().getSettingCount()); if (setting.getDisplay()) { af.viewport.featuresDisplayed.put(setting.getType(), new Integer( setting.getColour())); } } af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder; Hashtable fgtable; af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); fgtable.put(grp.getName(), new Boolean(grp.getDisplay())); } } if (view.getHiddenColumnsCount() > 0) { for (int c = 0; c < view.getHiddenColumnsCount(); c++) { af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view .getHiddenColumns(c).getEnd() //+1 ); } } af.setMenusFromViewport(af.viewport); Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view .getHeight()); //LOAD TREES /////////////////////////////////////// if (loadTreesAndStructures && jms.getTreeCount() > 0) { try { for (int t = 0; t < jms.getTreeCount(); t++) { Tree tree = jms.getTree(t); TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree .getNewick()), tree.getTitle(), tree.getWidth(), tree .getHeight(), tree.getXpos(), tree.getYpos()); tp.fitToWindow.setState(tree.getFitToWindow()); tp.fitToWindow_actionPerformed(null); if (tree.getFontName() != null) { tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree .getFontStyle(), tree.getFontSize())); } else { tp.setTreeFont(new java.awt.Font(view.getFontName(), view .getFontStyle(), tree.getFontSize())); } tp.showPlaceholders(tree.getMarkUnlinked()); tp.showBootstrap(tree.getShowBootstrap()); tp.showDistances(tree.getShowDistances()); tp.treeCanvas.threshold = tree.getThreshold(); if (tree.getCurrentTree()) { af.viewport.setCurrentTree(tp.getTree()); } } } catch (Exception ex) { ex.printStackTrace(); } } ////LOAD STRUCTURES if (loadTreesAndStructures) { for (int i = 0; i < JSEQ.length; i++) { if (JSEQ[i].getPdbidsCount() > 0) { Pdbids[] ids = JSEQ[i].getPdbids(); for (int p = 0; p < ids.length; p++) { for (int s = 0; s < ids[p].getStructureStateCount(); s++) { jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId())); jpdb.setId(ids[p].getId()); int x = ids[p].getStructureState(s).getXpos(); int y = ids[p].getStructureState(s).getYpos(); int width = ids[p].getStructureState(s).getWidth(); int height = ids[p].getStructureState(s).getHeight(); java.awt.Component comp = null; JInternalFrame[] frames = null; do { try { frames = Desktop.desktop.getAllFrames(); } catch (ArrayIndexOutOfBoundsException e) { // occasional No such child exceptions are thrown here... frames = null; try { Thread.sleep(10); } catch (Exception f) {}; } } while (frames==null); for (int f = 0; f < frames.length; f++) { if (frames[f] instanceof AppJmol) { if (frames[f].getX() == x && frames[f].getY() == y && frames[f].getHeight() == height && frames[f].getWidth() == width) { comp = frames[f]; break; } } } Desktop.desktop.getComponentAt(x, y); String pdbFile = loadPDBFile(file, ids[p].getId()); jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[] { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId() + "") }; if (comp == null) { String state = ids[p].getStructureState(s).getContent(); StringBuffer newFileLoc = new StringBuffer(state.substring( 0, state.indexOf("\"", state.indexOf("load")) + 1)); newFileLoc.append(jpdb.getFile()); newFileLoc.append(state.substring(state.indexOf("\"", state .indexOf("load \"") + 6))); new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel, newFileLoc.toString(), new java.awt.Rectangle(x, y, width, height)); } else if (comp != null) { StructureSelectionManager.getStructureSelectionManager() .setMapping(seq, null, pdbFile, jalview.io.AppletFormatAdapter.FILE); ((AppJmol) comp).addSequence(seq); } } } } } } return af; } private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al) { jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId()); Vector dseqs = null; if (ds == null) { // create a list of new dataset sequences dseqs = new Vector(); } for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) { Sequence vamsasSeq = vamsasSet.getSequence(i); ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs); } // create a new dataset if (ds == null) { SequenceI[] dsseqs = new SequenceI[dseqs.size()]; dseqs.copyInto(dsseqs); ds = new jalview.datamodel.Alignment(dsseqs); addDatasetRef(vamsasSet.getDatasetId(), ds); } // set the dataset for the newly imported alignment. if (al.getDataset() == null) { al.setDataset(ds); } } /** * * @param vamsasSeq sequence definition to create/merge dataset sequence for * @param ds dataset alignment * @param dseqs vector to add new dataset sequence to */ private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs) { jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId()); jalview.datamodel.SequenceI dsq = null; if (sq!=null && sq.getDatasetSequence()!=null) { dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence(); } String sqid = vamsasSeq.getDsseqid(); if (dsq==null) { // need to create or add a new dataset sequence reference to this sequence if (sqid != null) { dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid); } // check again if (dsq == null) { // make a new dataset sequence dsq = sq.createDatasetSequence(); if (sqid == null) { // make up a new dataset reference for this sequence sqid = seqHash(dsq); } dsq.setVamsasId(uniqueSetSuffix + sqid); seqRefIds.put(sqid, dsq); if (ds == null) { if (dseqs!=null) { dseqs.addElement(dsq); } } else { ds.addSequence(dsq); } } else { if (sq!=dsq) { // make this dataset sequence sq's dataset sequence sq.setDatasetSequence(dsq); } } } // TODO: refactor this as a merge dataset sequence function // now check that sq (the dataset sequence) sequence really is the union of all references to it //boolean pre = sq.getStart() < dsq.getStart(); //boolean post = sq.getEnd() > dsq.getEnd(); //if (pre || post) if (sq!=dsq) { StringBuffer sb = new StringBuffer(); String newres = jalview.analysis.AlignSeq.extractGaps( jalview.util.Comparison.GapChars, sq.getSequenceAsString()); if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength()) { // Update with the longer sequence. synchronized (dsq) { /*if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() - sq.getStart())); dsq.setStart(sq.getStart()); } if (post) { sb.append(newres.substring(newres.length() - sq.getEnd() - dsq.getEnd())); dsq.setEnd(sq.getEnd()); } */ dsq.setSequence(sb.toString()); } //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid System.err .println("DEBUG Notice: Merged dataset sequence"); // (" // + (pre ? "prepended" : "") + " " //+ (post ? "appended" : "")); } } } java.util.Hashtable datasetIds = null; private Alignment getDatasetFor(String datasetId) { if (datasetIds == null) { datasetIds = new Hashtable(); return null; } if (datasetIds.containsKey(datasetId)) { return (Alignment) datasetIds.get(datasetId); } return null; } private void addDatasetRef(String datasetId, Alignment dataset) { if (datasetIds == null) { datasetIds = new Hashtable(); } datasetIds.put(datasetId, dataset); } private void addDBRefs(SequenceI datasetSequence, Sequence sequence) { for (int d = 0; d < sequence.getDBRefCount(); d++) { DBRef dr = sequence.getDBRef(d); jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( sequence.getDBRef(d).getSource(), sequence.getDBRef(d) .getVersion(), sequence.getDBRef(d).getAccessionId()); if (dr.getMapping() != null) { entry.setMap(addMapping(dr.getMapping())); } datasetSequence.addDBRef(entry); } } private jalview.datamodel.Mapping addMapping(Mapping m) { SequenceI dsto = null; // Mapping m = dr.getMapping(); int fr[] = new int[m.getMapListFromCount() * 2]; Enumeration f = m.enumerateMapListFrom(); for (int _i = 0; f.hasMoreElements(); _i += 2) { MapListFrom mf = (MapListFrom) f.nextElement(); fr[_i] = mf.getStart(); fr[_i + 1] = mf.getEnd(); } int fto[] = new int[m.getMapListToCount() * 2]; f = m.enumerateMapListTo(); for (int _i = 0; f.hasMoreElements(); _i += 2) { MapListTo mf = (MapListTo) f.nextElement(); fto[_i] = mf.getStart(); fto[_i + 1] = mf.getEnd(); } jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit()); if (m.getMappingChoice() != null) { MappingChoice mc = m.getMappingChoice(); if (mc.getDseqFor() != null) { if (seqRefIds.containsKey(mc.getDseqFor())) { /** * recover from hash */ jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor())); } else { frefedSequence.add(new Object[] { mc.getDseqFor(), jmap }); } } else { /** * local sequence definition */ Sequence ms = mc.getSequence(); jalview.datamodel.Sequence djs=null; String sqid = ms.getDsseqid(); if (sqid!=null && sqid.length()>0) { /* * recover dataset sequence */ djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid); } else { System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference"); sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen) } if (djs==null) { /** * make a new dataset sequence and add it to refIds hash */ djs = new jalview.datamodel.Sequence(ms .getName(), ms.getSequence()); djs.setStart(jmap.getMap().getToLowest()); djs.setEnd(jmap.getMap().getToHighest()); djs.setVamsasId(uniqueSetSuffix + sqid); jmap.setTo(djs); seqRefIds.put(sqid, djs); } jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); addDBRefs(djs, ms); } } return (jmap); } public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs) { jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null, null, null); if (!keepSeqRefs) { clearSeqRefs(); jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); } else { uniqueSetSuffix = ""; } viewportsAdded = new Hashtable(); AlignFrame af = LoadFromObject(jm, null, false); af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); /* if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i